Figure 1. RNA polymerase–promoter interactions. (a) Structure of Thermus aquaticus RNA polymerase holoenzyme docked to promoter DNA, from studies by (Seth Darst) and co-workers. The locations of domains 2, 3 and 4 of the subunit (shown as orange ribbons) and their interactions with the –10, extended –10 and –35 elements (highlighted in red) are shown. Note that CTD and domain 1 are not seen in the T. aquaticus RNA polymerase structure. (b) Scheme that illustrates the subunit structure of RNA polymerase holoenzyme and the disposition of the different subunits that make contact with a bacterial promoter. The consensus sequences of the conserved promoter DNA elements are also shown. The subunit is comprised of 4 domains, and recognizes the –10, extended –10 and –35 elements. Each subunit consists of an N-terminal domain (NTD) and a C-terminal domain (CTD) joined by a linker. The two CTDs bind to A/T-rich UP-elements at many promoters. The and ¢ subunits comprise the active site of the enzyme. The subunit is thought to act as a chaperone to help the ¢ subunit to fold correctly. The horizontal arrow indicates the direction of transcription and its startpoint.

Figure 2. Mechanisms of transcription activation. (a) Class I activation. Class I activators bind upstream of their target promoters and recruit RNA polymerase by contacting the C-terminal domain of one of its subunits. (b) Class II activation. Class II activators bind close to the –35 element of target promoters and activate transcription by contacting domain 4 of the subunit. (c) Activation by pre-recruitment. Some activators bind directly to RNA polymerase before it binds to promoter DNA. Such activators can alter the DNA-binding specificity of RNA polymerase, for example by masking the DNA-binding surface of the subunit and replacing it with the DNA-binding domain of the activator. (d) Activation at ⁵⁴-dependent promoters. RNA polymerase containing ⁵⁴ can form a closed complex at a target promoter but is unable to form an open complex. Activators that function with this form of RNA polymerase bind to the DNA well upstream of the promoter, and, in order for them to contact RNA polymerase, a loop must form in the intervening DNA. The activators are ATPases, and direct contacts between the activator and ⁵⁴ drive a series of ATP-driven conformational changes that promote open-complex formation. (e) Activation by restructuring DNA. If the –10 and –35 elements are not properly aligned, RNA polymerase cannot initiate transcription. Transcription is stimulated by activators that bind between the –10 and –35 elements and alter the shape of the intervening DNA so that correct alignment is restored.

Figure 3. Activation by CRP. (a) Structure of E. coli CRP bound to its target DNA, from studies by (Tom Steitz) and co-workers. The figure shows a CRP dimer, with the three activating regions, that can contact RNA polymerase, highlighted. In this view, AR1 (shown in blue) is visible on the left-hand monomer, and AR2 (shown in green) and AR3 (shown in yellow) are visible on the right-hand monomer. (b) Activation by CRP at a Class I promoter. The CRP-binding site is located upstream of the RNA polymerase-binding site. AR1 of the downstream CRP subunit interacts with the C-terminal domain of one of the RNA polymerase subunits and so recruits RNA polymerase to the promoter. (c) Activation by CRP at a Class II promoter. The CRP-binding site is located at position –41.5. AR1 of the upstream CRP subunit contacts the C-terminal domain of one of the RNA polymerase subunits, AR2 of the downstream subunit contacts the N-terminal domain of one of the RNA polymerase subunits, and AR3 of the downstream subunit contacts domain 4 of the subunit.

Figure 4. Co-dependence mechanisms. Transcription initiation at many promoters requires two or more activators. The figure illustrates different mechanisms by which two activators (A and B) can cooperate to regulate a single promoter. (a) The binding of each activator to its target site in the DNA is dependent on the binding of the other. Only when both activators are present will a stable activator:DNA complex be formed. (b) The binding of one activator (B) may trigger the repositioning of the other (A), moving it from a location where it is unable to activate transcription, to a location where it is able to activate transcription. (c) The binding of one activator (B) to the promoter may alter the trajectory of promoter DNA such that the second activator (A) is able to make contact with RNA polymerase. (d) Two or more determinants are needed to provide sufficient contacts for RNA polymerase to be recruited, and these are provided by two or more transcription factors. e.g. a Class I activator can act in concert with a Class II activator (i), or with a second Class I activator (ii). (e) The second transcription activator (B) may counteract the action of a repressor (R) that is interfering with the function of the first activator (A).

Figure 5. Regulation of transcription factors. For transcription activation to act as a ‘genetic switch’, the activity of each transcription activator must be controlled. The figure illustrates different mechanisms used to ensure that activators switch on genes in response to the correct signal. (a) Regulation by binding of a small ligand. Some activators are toggled between an active and inactive form by binding a small signal molecule, such as cyclic adenosine monophosphate (cAMP). Typically, the small molecule causes a conformational change that affects an essential function such as DNA-binding specificity. In this example, interaction with a small ligand converts the activator from an inactive form that is unable to bind to its target sequence to an active, sequence-specific DNA-binding form. (b) Regulation by covalent modification. Some activators are converted between active and inactive forms by covalent modification (e.g. phosphorylation by a kinase that senses a particular signal). Typically, the covalent modification affects an essential function such as DNA-binding specificity. In this example, the activator is converted from an inactive form, that is unable to bind to its target sequence, to an active, sequence-specific DNA-binding form by phosphorylation of its receiver module. (c) Regulation by intracellular protein concentration. The ability of some activators to regulate gene expression is controlled by their concentration. In this example, the activator is produced constitutively and its steady state concentration is kept low because the activator is rapidly degraded by proteases (P). If the proteases are prevented from degrading the activator its concentration in the cell rapidly rises. (d) Regulation by restriction of cellular location. The activity of some regulatory proteins is controlled by proteins that sequester them to locations from which they cannot activate transcription. In this example, ²⁸ is prevented from binding to RNA polymerase by a complex of proteins that hold it at the cell membrane. In response to an appropriate signal, the complex releases ²⁸, allowing it to activate transcription. (e) Regulation by anti- factors. Anti- factors regulate factor activity by forming a complex that prevents the factor binding to RNA polymerase. In response to an appropriate signal, the anti- factor releases the factor, allowing it to activate transcription of its target genes. The mechanism by which the :anti- complex is disrupted often involves a third protein, termed an anti-anti-, which binds to the anti- factor more tightly than the factor. This mechanism is often referred to as ‘partner switching’.